As I generate the entity classes from hbm files, I use base classes with @MappedSuperclass:

@MappedSuperclass
public class MyEntityBase {
    ....
}

@Entity
public class MyEntity extends MyEntityBase {
    ....
}

In an entityGraph, I can use basic attributes defined in the base class without problems.
Adding any collection as subgraph throws a MappingException:

org.hibernate.MappingException: Unknown entity: MyEntityBase

See the attached test case for details, too